Experiment set14IT010 for Pseudomonas fluorescens SBW25-INTG

D,L-Malic Acid (C) and Ammonium chloride (N); with TAPS; with Sodium chloride

Group: stress
Media: MTM_noNitrogen_noCarbon + D,L-Malic Acid (20 mM) + Ammonium chloride (10 mM) + Sodium Chloride (400 mM), pH=8.5
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on September 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM TAPS sodium salt, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 24 genes in this experiment

For stress D,L-Malic Acid in Pseudomonas fluorescens SBW25-INTG

For stress D,L-Malic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Arginine and Ornithine Degradation	1
Biogenesis of c-type cytochromes	1
Butanol Biosynthesis	1
Cysteine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
DNA repair, bacterial	1
Experimental tye	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Periplasmic disulfide interchange	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
Queuosine-Archaeosine Biosynthesis	1
TCA Cycle	1
Valine degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Glycerophospholipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Biosynthesis of terpenoids and steroids
• Fatty acid biosynthesis
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Geraniol degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Ethylbenzene degradation
• One carbon pool by folate
• Methane metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
D-serine degradation	3	3	2
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
glycine betaine degradation III	7	7	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
dTMP de novo biosynthesis (mitochondrial)	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
oleate biosynthesis III (cyanobacteria)	3	2	1
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
phosphatidate biosynthesis (yeast)	5	3	1
fatty acid salvage	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
phosphatidylglycerol biosynthesis I	6	5	1
phosphatidylglycerol biosynthesis II	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
palmitoyl ethanolamide biosynthesis	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
stigma estolide biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
partial TCA cycle (obligate autotrophs)	8	8	1
purine nucleobases degradation II (anaerobic)	24	16	3
anandamide biosynthesis II	8	2	1
folate transformations III (E. coli)	9	9	1
TCA cycle VII (acetate-producers)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle I (prokaryotic)	10	9	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
folate transformations II (plants)	11	10	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
anandamide biosynthesis I	12	3	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of phospholipid biosynthesis II (plants)	28	9	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
oleate β-oxidation	35	33	1
superpathway of chorismate metabolism	59	42	1